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Though President Obama has repeatedly urged that science guide environmental decisions, regulators inside the Environmental Protection Agency secretly worked with tribal and environmental activists to preempt a full review of an Alaskan mine and veto the project before the owners’ permits could be considered, internal memos show.

Charged with being neutral arbiters, EPA officials instead began advocating for a preemptive veto of the Pebble Mine project in western Alaska as early as 2008, long before any scientific studies were conducted or the permit applications for the project were even filed, the emails obtained by The Washington Times show.

“As you know I feel that both of these projects (Chuitna and Pebble) merit consideration of a 404C veto,” EPA official Phillip North wrote in an email suggesting that the mining project’s rejection be added to the agenda of an agency retreat in summer 2009.

EPA wouldn’t even announce the beginning of a scientific review of Pebble Mine until 2011, two years after Mr. North’s email, but discussion of a pre-emptive veto dominated internal discussions inside the agency for much of the three years beforehand.

At the same time, EPA officials had regular contacts with potential opponents of the mining project, coordinating activities with environmentalists and even coaching local tribes on how they could strengthen their case opposing the project.

“Tribes have a very special role in Pebble issues because of government-to-government relations,” Mr. North wrote to an Alaskan tribal leader in June 2010. “EPA takes that very seriously. I encourage you to develop that relationship as much as you can.”

The efforts to get EPA to veto the project before the Army Corps of Engineers could evaluate the engineering and scientific impacts reached all the way to top officials in Washington.

A presentation prepared in 2010 for then-EPA Administrator Lisa P. Jackson made clear that a preemptive veto “had never been done before in the history” of the Clean Water Act and could risk litigation.

EPA eventually conducted a narrow scientific review and preemptively vetoed the mine project this February, before the Army Corps of Engineers could decide the permits for the project on the scientific and technical merits.

The decision has become one of the most controversial in recent EPA history, prompting the owners of the proposed mine, members of Congress and the state of Alaska to request a formal investigation by the EPA’s internal watchdog, the inspector general.

“The state is concerned that actual bias within the agency induced EPA to invoke a novel interpretation of its statutory authority to conduct the assessment and led to the development of an assessment that contains findings likely tainted by that bias,” Alaska Attorney General Michael C. Geraghty wrote Inspector General Arthur Elkins on Feb. 3.

Republicans on the House Oversight and Government Reform Committee made a similar request after reviewing some of the same documents obtained by The Times. “Taking such unprecedented federal agency action with predetermined conclusions is not sound government practice and delegitimizes other necessary regulatory action undertaken by the EPA,” the lawmakers argued.

EPA officials defend the process, saying the documents reflect internal deliberations and not necessarily how the final decisions were made.

“There may be emails that people point to with staff in EPA, but this is a large organization and you should look at what the leadership of EPA has actually done. We haven’t made up our minds at all on how this process will ends, this is just a process,” the agency said in a statement given to The Times. “We believe that any action taken should be based on the science.”

Environmental activists in the region accused Pebble Mine’s backers of raising old, discredited arguments to push through a project that they say will decimate the local fishing industry and kill thousands of jobs.

Pebble Mine’s backers “continually and deliberately fail to mention that EPA’s involvement in Bristol Bay came at the request of the people of Alaska and the fishermen of Bristol Bay ,” Katherine Carscallen, sustainability director for the Bristol Bay Regional Seafood Development Association, said in a statement Wednesday on the organization’s website. “We know enough about [Pebble Limited Partnership‘s] plans — from its own documents — to conclude beyond doubt that development of a mine like Pebble would result in unacceptable adverse effects on the Bristol Bay watershed.”

Flashpoint

But Tom Collier, a Clinton administration official who now serves as CEO of Pebble Partnership that is seeking to build the mine, said there was no legal reason for the EPA to make its decision before the Army Corps of Engineers completed its scientific review and issued an environmental impact report.

“Then EPA has every right under the statute to step in whether they so choose, but at least at that time they’ve got a strong record that’s been developed out of a rigorous, transparent and well-used practice,” he said in an interview.

The Pebble Mine is the latest flashpoint between industries eager to tap Alaska’s rich bounty of minerals, metals and fuels beneath the earth and those who want to protect the state’s pristine landscape.

The controversy surrounds Bristol Bay in Alaska, one of the most popular commercial fishing spots in the world. The EPA estimates that the area produces roughly half of the world’s population of wild sockeye salmon, an economic boon valued at $300 million in 2009 and a key part of the multibillion-dollar fishing industry. It’s described as the largest fishing spot in the Pacific Ocean.

But the bay also has an abundance of other valuable commodities: gold, silver and copper.

Under a compromise that helped create the Clean Water Act in 1972, the Army Corps of Engineers has responsibility for conducting environmental impact assessments of potential projects — information that the EPA then uses to reach its decisions.

The EPA officials reviewing Pebble project, however, argued that they should decide the project at the outset and not wait for the corps.

Such an approach advocated in the internal emails conflicts with Mr. Obama’s often-stated goal that such decisions be made on scientific merits alone. “Science holds the key to our survival as a planet and our security and prosperity as a nation. It’s time we once again put science at the top of our agenda and worked to restore America’s place as the world leader in science and technology,” the president urged in one of his first radio addresses after winning the 2008 election.

The 2010 presentation prepared for Ms. Jackson, the president’s first EPA chief, laid out “options to influence the project” and produce a veto before the corps completed its environmental assessment.

Officials debated the pros and cons if the EPA rejected the proposal based a section of the Clean Water Act that “authorizes EPA to prohibit, restrict or deny the discharge of dredged or fill material at defined sites in waters of the United States.”

Traditionally waiting until permits were filed and scientific studies were completed would “generate considerable information informing the decision,” the document for Ms. Jackson stated. But officials worried that waiting would risk the EPA being able to veto only the single mine and not prevent any future construction in the region.

EPA officials also identified as a con the fact that proponents of the project would spend “tens of millions of dollars” making the case for the project before the agency could weigh in with its decision.

Many of the concerns identified in the document dealt with politics and process, and not the science.

Tipped off?

When EPA finally announced it would conduct its own scientific assessment in 2011, it said it had done so at the request of tribes. In fact, EPA officials had long debated the veto before that and reached out to the tribes preemptively, tipping them off that the EPA was considering a preemptive veto.

“We have been discussing 404 (c) quite a bit internally at all levels of EPA,” Mr. North wrote an attorney for a tribal company in August 2010. “This letter will certainly stoke the fire.”

Likewise, EPA officials briefed the conservation group Trout Unlimited, another mine opponent, about its plans.

One of the clearest signs that EPA had predetermined it would kill the project came in the form of a 2011 budget request that sought money to pursue the 404(c) veto.

Officials at other federal agencies with roles in the mining review process were talking as early as 2010 that an EPA veto was a fait accompli.

Mr. North has briefed top EPA officials in Washington and “believes EPA leaders have decided to proceed and they are just deciding when,” Fish and Wildlife Service biologist Phil Brna wrote in an email in September 2010.

An investigation of the timeline could set the stage for legal action by the mine proponents, who argue that the EPA had no reason to pre-empt the normal process and prevent a full scientific review.

Mr. Collier, the CEO of the mine company and a former regulator himself under Clinton Interior Secretary Bruce Babbitt, scoffs at the rationale that the EPA has used in claiming it was simply trying to protect the environment and local tribes’ fishing livelihoods.

“The best way to determine whether or not that’s the case is to do an environmental impact statement,” he said. “If they’re concerned about this, why won’t they allow the science they’re relying on to go through that process?”